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Table of Contents

All samples processed together

  • Figure 1: MDS plot, all samples

  • Figure 2: Barplot of Total DEGs

Testing potential outlier samples

  • Figure 3: PCA of GR.F CxDf DEGs

  • Figure 4: PCA of GR.F CxOE DEGs

  • Figure 5: PCA of GR.FC x WT.FC DEGs

  • Figure 6: PCA of WT.F CxDf DEGs

  • Figure 7: PCA of WT.F CxOE DEGs

  • Figure 8: PCA of TktDfGR.F x TktDfWT.F DEGs

Male and female samples processed together with TEs and outlier libraries removed

  • Figure 9: MDS plot, all samples

  • Figure 10: Barplot of Total DEGs

Male and Female samples processed separately with TEs and outlier libraries removed

  • Figure 11: MDS plot of female samples only

  • Figure 12: MDS plot of male samples only

  • Figure 13: Barplot of Total DEGs

  • Figure 14: Barplot of Total DEGs for each comparison under the different trimming conditions




Conclusion: GR.F3, WT.F3 and TktDfWT.F3 are outlier libraries that should be removed before further analysis but there is no need to process male and female samples separately







Do the samples group by condition?

Figure 1: MDS plot using all samples. Of these, samples GR.F3, WT.F3 and TktDfWT.F3 stand out as potential outliers.







Figure 2: Barplot of Total DEGs observed with edgeR when using all samples.







Is the expression profile for GR.F3 an outlier in genes found DE GR.FC and GR.FDf?

Figure 3: PCA of GR.F CxDf DEGs. Testing if GR.F3 is an outlier library.







Is the expression profile for GR.F3 an outlier in genes found DE GR.FC and GR.FOE?

Figure 4: PCA of GR.F CxOE DEGs. Testing if GR.F3 is an outlier library.







Are the expression profiles for GR.F3 and WT.F3 outliers in genes found DE GR.FC and WT.FC?

Figure 5: PCA of GR.FC x WT.FC DEGs. Testing if GR.F3 and WT.F3 are outlier libraries.







Are the expression profiles for WT.F3 and TktDfWT.F3 outliers in genes found WT.FC and TktDfWT.F?

Figure 6: PCA of WT.F CxDf DEGs. Testing if WT.F3 and TktDfWT.F3 are outlier libraries.







Is the expression profile for WT.F3 an outlier in genes found DE WT.FC and WT.FOE?

Figure 7: PCA of WT.F CxOE DEGs. Testing if WT.F3 is an outlier library.







Is the expression profile for TktDfWT.F3 an outlier in genes found DE TktDfGR.F and TktDfWT.F?

Figure 8: PCA of TktDfGR.F x TktDfWT.F DEGs. Testing if TktDfWT.F3 is an outlier library.







Does processing the samples after removing the 3 outlier libraries and TEs improve sample normalization?

Figure 9: MDS plot using all samples, with the TEs and outlier libraries removed.







Figure 10: Barplot of Total DEGs found when using all samples with the TEs and outlier libraries removed.







Does sex specifically processing the samples after removing the 3 outlier libraries and TEs improve sample normalization?

Figure 11: MDS plot when the female samples are processed alone. The TEs and outlier libraries are removed.







Figure 12: MDS plot when the male samples are process alone only. The TEs are removed.







Figure 13: Barplot of Total DEGs when male and female samples are processed separately. The TEs and outlier libraries were removed.







How do the different processing methods alter the number of total DEGs?

Figure 14: Barplot of Total DEGs for each comparison under the different trimming conditions. Different trimming conditions were: (1) all samples processed together with no TEs or outlier libraries removed; (2) trimmed data with TEs and outlier libraries removed, male and female samples processed together; (3) trimmed data with TEs and outlier libraries removed, male and female samples processed separately.